bin/hrquest.sh

   1 #!/bin/sh -l
   2
   3 function unziptar {
   4         echo "unziptar $1"
   5         zipname=`echo $1 | grep '\.zip'`
   6         echo $zipname
   7         tarname=`echo $1 | grep '\.tar'`
   8         echo $tarname
   9         tgzname=`echo $1 | grep '\.tgz'`
  10         echo $tgzname
  11         if [ "x$zipname" != "x" ]
  12                 then
  13                 echo "ZIP File"
  14                 unzip -j $1 -d data
  15         else
  16                 if [ "x$tarname" != "x" ]
  17                         then
  18                         echo "TAR File"
  19                         COMP=`tar -tvf $1 | awk 'END{print}' |   awk -F' ' '{print $NF}' | awk -F'/' '{print NF-1}'`
  20                         tar -xvf $1 --strip-components=${COMP} -C data
  21                 else
  22                         if [ "x$tgzname" != "x" ]
  23                                 then
  24                                 echo "TGZ File"
  25                                 COMP=`tar -tvf $1 | awk 'END{print}' |   awk -F' ' '{print $NF}' | awk -F'/' '{print NF-1}'`
  26                                 tar -zxvf $1 --strip-components=${COMP} -C data
  27                         else
  28                                 echo "Unknown File Type"
  29                                 exit 6
  30                         fi
  31                 fi
  32         fi
  33
  34         if [ $? != 0 ]
  35                 then
  36                 echo "A problem occurred while untargzing the input: giving up!"
  37                 exit 2
  38         fi
  39 }
  40
  41 function checkdir {
  42         lfc-ls $1 > /dev/null
  43         if [ $? != 0 ]
  44         then
  45                 echo "Directory $1 not found, creating it!"
  46                 lfc-mkdir -p $1
  47                 #exit 6
  48         fi
  49 }
  50
  51
  52 function downloadDir {
  53         checkdir $1
  54         LOCALDIR=`basename $1`
  55         mkdir -p ${LOCALDIR}
  56         for i in `lfc-ls $1 | grep -v garbage`
  57         do
  58                 lcg-cp -v lfn:$1/$i file:$PWD/${LOCALDIR}/$i
  59                 if [ $? != 0 ]
  60                 then
  61                         echo "lcg-cp failed: trying once more"
  62                         lcg-cp -v lfn:$1/$i file:$PWD/${LOCALDIR}/$i
  63                         if [ $? != 0 ]
  64                         then
  65                                 echo "Unable to download file lfn:$1/$i: giving up."
  66                                 exit 1
  67                         fi
  68                 fi
  69         done
  70 }
  71
  72 function downloadFile {
  73         local fname=`basename $1`
  74         test -f $fname
  75         CODE=$?
  76         if [ ${CODE} != 0 ]
  77         then
  78
  79                 lcg-cp -v lfn:$1 file:$PWD/$fname
  80                 if [ $? != 0 ]
  81                 then
  82                         echo "lcg-cp failed: trying once more"
  83                         lcg-cp -v lfn:$1 file:$PWD/$fname
  84                         if [ $? != 0 ]
  85                         then
  86                                 echo "Unable to download file lfn:$1: giving up."
  87                                 exit 1
  88                         fi
  89                 fi
  90         else
  91                 echo "File $fname already exists locally"
  92         fi
  93 }
  94
  95 in=$@
  96 suffix=" ] "
  97 echo $in | grep '\['
  98 CODE=$?
  99 if [ ${CODE} != 0 ]
 100 #simple arguments, no arrays
 101 then
 102   SIGFILE=$1
 103   PARAMFILE=$2
 104   INFOLDER=$3
 105   RESDIR=$4
 106 else
 107 #split inputs based on [] and retrieve contents
 108   SIGFILE=`echo $in | awk -F'\\\[' '{print $2}' | awk -F'\\\]' '{print $1}'`
 109   mySigArray=( $SIGFILE )
 110   PARAMFILE=`echo $in | awk -F'\\\]' '{print $2}' | awk -F' ' '{print $1}'`
 111   INFOLDER=`echo $in | awk -F'\\\]' '{print $2}' | awk -F' ' '{print $2}'`
 112   RESDIR=`echo $in | awk -F'\\\] ' '{print $2}' | awk -F' ' '{print $3}'`
 113
 114   echo "Resdir is $RESDIR"
 115
 116 fi
 117
 118
 119 DATADIR=`dirname ${INFOLDER}`
 120
 121 echo "Downloading inputs"
 122
 123 downloadFile $PARAMFILE
 124
 125 ((n_elements=${#mySigArray[@]}, max_index=n_elements - 1))
 126 for ((i = 0; i <= max_index; i++)); do
 127   downloadFile ${mySigArray[i]}
 128 done
 129
 130
 131 #COMPDATA=$4
 132 #RESDIR=$5
 133 #preparing input data
 134 #export LD_LIBRARY_PATH=/usr/local/matlab/MCR/v84/runtime/glnxa64:/usr/local/matlab/MCR/v84/bin/glnxa64:/usr/local/matlab/MCR/v84/sys/os/glnxa64:$LD_LIBRARY_PATH
 135 #export XAPPLRESDIR=/usr/local/matlab/MCR/v84/X11/app-defaults
 136
 137 hname=`hostname`
 138 if [ "${hname}" != "moteur1.grid.creatis.insa-lyon.fr" ] && [ "${hname}" != "moteur2.grid.creatis.insa-lyon.fr" ]
 139 then
 140         echo "hrquest not yest supported on grid resources"
 141
 142 else
 143         export PATH=/usr/local/hrquest:$PATH
 144         export LD_LIBRARY_PATH=/usr/local/hrquest/lib:$LD_LIBRARY_PATH
 145         echo "LD_LIBRARY_PATH is $LD_LIBRARY_PATH"
 146 fi
 147
 148
 149 #export LFC_HOST=lfc-biomed.in2p3.fr
 150 #export LCG_GFAL_INFOSYS=cclcgtopbdii02.in2p3.fr:2170
 151
 152 #echo "whoami, Printing env"
 153 #whoami
 154 #env
 155
 156 echo "result dir is $RESDIR"
 157 checkdir $RESDIR
 158
 159 #preparing comparison data
 160 #mkdir ${DATADIR}
 161 #cd ${DATADIR}
 162 downloadDir ${INFOLDER}
 163 #cd ..
 164
 165 echo "pwd is `pwd`, creating outputs folder"
 166 mkdir outputs
 167 #launching program
 168 echo "launching the program"
 169 ((n_elements=${#mySigArray[@]}, max_index=n_elements - 1))
 170 PF=`basename ${PARAMFILE}`
 171 for ((i = 0; i <= max_index; i++)); do
 172   echo "launching the program for i = $i"
 173   SIG=`basename ${mySigArray[i]}`
 174   echo "hrquestCml -f $PF $SIG"
 175   hrquestCml -f $PF ${SIG}
 176   CODE=$?
 177   if [ ${CODE} != 0 ]
 178   then
 179     echo "Execution failed with code ${CODE}"
 180     exit ${CODE}
 181   fi
 182   #echo "mySigarray is ${SIG}"
 183   basefilename=`basename ${SIG%.*}`
 184   mv ${basefilename}_* outputs/
 185 done
 186
 187
 188 RESULT=results.tgz
 189 LFN=${RESDIR}/${RESULT}
 190 lfc-ls ${LFN}
 191         if [ $? = 0 ]
 192         then
 193                 echo "deleting previous ${LFN}"
 194                 lcg-del -a lfn:/${LFN}
 195                         if [ $? != 0 ]
 196                         then
 197                                 echo "not able to lcg-del lfn:/${LFN}, renaming it"
 198                                 d=`date -d "" +%s`
 199                                 lfc-rename ${LFN} ${LFN}-garbage-${d}
 200                         fi
 201         fi
 202
 203
 204
 205 tar -czvf $RESULT outputs
 206 test -f ${RESULT}
 207 CODE=$?
 208 if [ ${CODE} != 0 ]
 209 then
 210     echo "Execution failed: exiting with code ${CODE} since ${RESULT} does not exist"
 211     exit ${CODE}
 212 else
 213     echo "Execution done, ${RESULT} created."
 214 fi
 215